[phenixbb] NCS problem

Daniel Frey freyd at bioc.unizh.ch
Tue Apr 22 07:34:41 PDT 2008

Dear Robert,

there was a post on it in the phenixbb that this trick wont work in  
phenix. The nonbonded interactions are still valid and therefore the  
two glycerols are moved apart. I have a similar problem with a lysine  
side chain clashing into the symmetry related side chain of the same  
amino acid. I am still trying to model it correctly.
Best wishes Daniel

The original post was:

Hi Morton,

 > I have a symmetrical ligand, malonate -OOCCCOO-, that binds right  
on the
 > crystallographic axis of a C2 structure. Is the correct approach to  
 > the occupancy to 0.5 and then refine or is there a better way to  
handle is
 > in Phenix?

The 0.5 trick currently doesn't work in phenix.refine since we don't
provide a way to turn off nonbonded interactions between symmetry

However, we fully support handling of atoms on special positions and
bonds involving symmetry operations. For this to work, you have to give
only an asymmetric unit worth of atoms, i.e. in your case half of your
molecule. Is the C in the middle exactly on the two-fold axis? If so,
delete these atoms from the PDB file:


Then use the custom bond and angle feature (for the angles you'll need
the 2007_04_06 CCI Apps) to define the required bonds and angles,
including the bonds to the protein. I hope it is straightforward.
If not, could you send me the fragments from you pdb file with the
malonate and the piece of protein it is linked to? Then I could
work out the bond and angle definitions for you.

On 22.04.2008, at 15:42, Bobby Huether wrote:

> Hello,
> My structure contains 2 protein molecules in the asymmetric unit,  
> and they
> are related by 2-fold rotational NCS to form a dimer. The   
> refinement is
> nearing completion (1.7 A) and the solvent molecules are now being  
> included.
> A blob of density has been tentatively identified as being occupied by
> glycerol, which was present as the cryo-protectant. The issue is  
> that this
> blob of density lies on the 2-fold NCS rotation axis, and so we need  
> to use
> 2 glycerol molecules within this density, each at 0.5 occupancy, to  
> conform
> to the NCS symmetry. This blob of density lies in a surface pocket  
> formed by
> residues from both NCS-related proteins.
> When we build in the 2 glycerol molecules and then use  
> phenix.refine, the
> two glycerols are pushed out of density. Presumably this is because
> phenix.refine is interpreting this situation as two glycerol molecules
> sitting on top of on another rather than interpreting it as being a  
> model
> for a disordered ligand.
> Can phenix.refine handle this situation?
> Thanks,
> Robert
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Daniel Frey
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich

freyd at bioc.unizh.ch
Tel: +41446355558


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